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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag

Basic information

species Oryza sativa
transcript LOC_Os07g14150.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14150.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G008216_T03 (Zea mays), 5'ss of exon 2
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa------aataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttgggg--cgctttt----aaggtcttccagaagaactgctt-agtgttaacttgagttttggaaaaatttacag----------------------------------------------
|||||||||||||||||||||||||||| ||||||||||||||||||||| | || |||||| |||| |       | ||||  |  |  ||||||||  |    |||    |  || |||||||  ||| | |    | ||       ||  ||    || | | || |     || | || |   ||   |  | |||      |  | ||||                                              
TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAGgtgagagcattgctgcagtaataataat-tattagtctaattcccttg--tcgttgcacagctttacctgctggcagaagttcaacattgccattgaccaatgacctctaaggtcacagtttcaccatttggtaaaatttgcttttatgtaacagcagcaagaaaactgatctaagacacgcattttggtgaattttgcag

upper sequence: LOC_Os07g14150.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G082924_T01 (Zea mays), 5'ss of exon 2
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgct--tctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggt--------gatttggggcgcttttaaggtcttccaga--agaactgcttagtgtt-----aacttgagttttggaaaaatttacag----------------------------------------
||||||||||||||||||||||||||||||||||||||||||||| || ||| || |||||| |||  |     ||| |  | |   ||    ||| |   | | |   ||||    ||| |   | |  |||        ||  |||   |    || | |||   ||   | |  | ||     ||     ||||||   ||  | ||      ||                                         
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAGgtgagaacattgccatggtatttttttttgtagttccctcgtagttgcacagctttacttactgagataaggtcaacactggacatggcctggacctatgatctctaaggtcacagtttctcgcctttggtaaaacttgctcttatgtaacgacagcaagaaaactgatctaagacctgcattttggtgaattttgcag

upper sequence: LOC_Os07g14150.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G04720.1 (Glycine max), 5'ss of exon 1
----------------------------------------TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag
                                        |||||||  | |||||||||||  ||||||| ||| |||| ||||||||||| || ||||||||           ||||||||||| |||    |||| ||  | ||  ||   | ||||  | || |       |||     |||||  |  |      ||  |  |||| |  |                          
TATTTATGTTTTTTTTTTCTTTTCTTTTTTATTACTTCAGTTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaa-----------tgcttctgcat-agt----tcagatttct-tgttgcaatgttttc-ttattagttatccatggctgatttttattgattcattttaggccatcttatttattg------------------------

upper sequence: LOC_Os07g14150.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G04720.2 (Glycine max), 5'ss of exon 2
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag
|||||||  | |||||||||||  ||||||| ||| |||| ||||||||||| || ||||||||           ||||||||||| |||    |||| ||  | ||  ||   | ||||  | || |       |||     |||||  |  |      ||  |  |||| |  |                          
TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaa-----------tgcttctgcat-agt----tcagatttct-tgttgcaatgttttc-ttattagttatccatggctgatttttattgattcattttaggccatcttatttattg------------------------

upper sequence: LOC_Os07g14150.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G17790.1 (Glycine max), 5'ss of exon 2
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag
| |||||  | |||||||||||  ||||||| ||| |||| |||||||||||||| ||||||||   |     | || ||     | | |  |  | |     | | |     || | ||  ||  ||  |  | | |    |  |||||| |||| | | |   ||                                   
TCGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCACCAGGAAGgtaatgcttctgcattgttt-----tgatttcttgctgcaatgttttcttattagttatccatggctgatttttattga-tacacttaaggccttc-atatgtcttg-----------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88326542|gb|CI644645.1|CI644645
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33684397|gb|CF312636.1|CF312636
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAAATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88376916|gb|CI639241.1|CI639241
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33684446|gb|CF312685.1|CF312685
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33670472|gb|CF298711.1|CF298711
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCTTTTTCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88348203|gb|CI637664.1|CI637664
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33681048|gb|CF309287.1|CF309287
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCCAGTTGAAGAAGCG
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGC-AGTTGAAGAAGCG
EST: gi|33681325|gb|CF309564.1|CF309564
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33680862|gb|CF309101.1|CF309101
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|55413799|gb|CV726175.1|CV726175
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88576116|gb|CI670261.1|CI670261
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88324909|gb|CI644920.1|CI644920
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAACAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33682363|gb|CF310602.1|CF310602
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88328922|gb|CI647002.1|CI647002
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCCAGTTGAAGAAGCG
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGC-AGTTGAAGAAGCG
EST: gi|33670643|gb|CF298882.1|CF298882
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCANTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33820665|gb|CF336142.1|CF336142
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATAAAG                         CTGTGCAAGATACAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33679899|gb|CF308138.1|CF308138
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88575933|gb|CI670078.1|CI670078
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33683865|gb|CF312104.1|CF312104
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGN
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCG-
EST: gi|88351621|gb|CI628841.1|CI628841
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88327608|gb|CI646801.1|CI646801
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33654855|gb|CF277469.1|CF277469
EST:     AAAGGGTGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|58592974|gb|CF991282.1|CF991282
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAACGATAGAGACCACAAATTCTTGACAAAAGCAGTGTGAAGAAGC
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAA-GATAGAGACCACAAATTCTTGACAAAAGCAGT-TGAAGAAGC
EST: gi|88334769|gb|CI647151.1|CI647151
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|33680734|gb|CF308973.1|CF308973
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
EST: gi|88337228|gb|CI628314.1|CI628314
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG                         CTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaa ... aaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag

- - - - - - AGGATG
- - - - - - - GATGGA